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Detailed information for vg1001933162:
| Variant ID: vg1001933162 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933162 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCTTCACCATCCTCTCGAAGCGTCGCAATATTCTAAGCCAGAAGTGAACATTATGGTTCCTTCTAAGCATGTCAGATATCATATTGGCTGTTATCAATG[A/T]
TCCACCCAATACTACTGCAAGATCATTTGCAACTGAGACCATCTTTGGATGGTCCTTTTGGTCGGTCGCTAGCATCTTGAAAAGGTAGCTGTACTCCTCC
Reverse complement sequence
GGAGGAGTACAGCTACCTTTTCAAGATGCTAGCGACCGACCAAAAGGACCATCCAAAGATGGTCTCAGTTGCAAATGATCTTGCAGTAGTATTGGGTGGA[T/A]
CATTGATAACAGCCAATATGATATCTGACATGCTTAGAAGGAACCATAATGTTCACTTCTGGCTTAGAATATTGCGACGCTTCGAGAGGATGGTGAAGAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.50% | 3.40% | 0.30% | 14.81% | NA |
| All Indica | 2759 | 72.60% | 5.60% | 0.40% | 21.42% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 64.70% | 0.00% | 1.12% | 34.20% | NA |
| Indica I | 595 | 61.00% | 0.00% | 0.50% | 38.49% | NA |
| Indica II | 465 | 82.20% | 3.40% | 0.22% | 14.19% | NA |
| Indica III | 913 | 70.60% | 10.10% | 0.11% | 19.17% | NA |
| Indica Intermediate | 786 | 78.00% | 5.90% | 0.76% | 15.39% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 85.60% | 7.80% | 0.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933162 | A -> T | LOC_Os10g04160.1 | missense_variant ; p.Ser241Thr; MODERATE | nonsynonymous_codon ; S241T | Average:41.396; most accessible tissue: Zhenshan97 young leaf, score: 75.039 | benign  |
1.134 |
DELETERIOUS | 0.03 |
| vg1001933162 | A -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:41.396; most accessible tissue: Zhenshan97 young leaf, score: 75.039 | N | N | N | N |